# Frontiers in Plant Science
**Computational Basics for Plant Biology**

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**Jason Williams, CSHL**
(e) [e-mail], (t) @JasonWilliamsNY

**Zoom** (for screensharing): [https://cshl-dnalc.zoom.us/j/93139573652?pwd=RUM1SFo3RlJoNzVpVmtJSjd0REJkdz09](https://cshl-dnalc.zoom.us/j/93139573652?pwd=RUM1SFo3RlJoNzVpVmtJSjd0REJkdz09)

**Google sheet of instances**: [Instances](https://docs.google.com/spreadsheets/d/1B3Q_HOIVtUaNhpHAz7eju_9K1NTJtRmqkv_GeLrPsfM/edit?usp=sharing)

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[toc]

## Resources

### Data/knowledge management

\* - FOSS [Data Management intro](https://cyverse-foss.readthedocs-hosted.com/en/latest/03_managing_data.html#)

- Markdown: [https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet](https://github.com/adam-p/markdown-here/wiki/Markdown-Cheatsheet)
- ReadTheDocs/mk-docs: [https://readthedocs.com/](https://readthedocs.com/), [https://mkdocs.readthedocs.io/en/stable/](https://mkdocs.readthedocs.io/en/stable/)
- FairSharing: [https://fairsharing.org/](https://fairsharing.org/)
- FAIR Principles paper: [https://www.nature.com/articles/sdata201618](https://www.nature.com/articles/sdata201618)
- Data Stewardship Wizzard: [https://ds-wizard.org/](https://ds-wizard.org/)
- Example [DMPs](https://www.lib.ncsu.edu/do/data-management/elements-of-a-dmp)

### Reproducibility

- GitHub: [github.com/](github.com/)
- Conda: [https://docs.conda.io/en/latest/](https://docs.conda.io/en/latest/)
- Bioconda: (https://bioconda.github.io/)
- Docker: [https://www.docker.com/](https://www.docker.com/)
- Ten Simple Rules on Dockerfiles: [https://journals.plos.org/ploscompbiol/article/comments?id=10.1371/journal.pcbi.1008316](https://journals.plos.org/ploscompbiol/article/comments?id=10.1371/journal.pcbi.1008316)
- Biocontainers: [https://biocontainers.pro/](https://biocontainers.pro/)
- Jupyter: [https://jupyter.org/](https://jupyter.org/)
- Snakemake: [https://snakemake.readthedocs.io/en/stable/](https://snakemake.readthedocs.io/en/stable/)

### Software and coding skills

\* - Software Carpentry [Plotting and Programming in Python](http://swcarpentry.github.io/python-novice-gapminder/)

- Software Carpentry: [https://software-carpentry.org/](https://software-carpentry.org/)
- Data Carpentry: [https://datacarpentry.org/](https://datacarpentry.org/)
- Bioconductor: [http://bioconductor.org/](http://bioconductor.org/)

### Computational resources

- CyVerse: [https://cyverse.org/](https://cyverse.org/)
- JetStream2: [https://jetstream-cloud.org/](https://jetstream-cloud.org/)
- Galaxy: [https://usegalaxy.org/](https://usegalaxy.org/)

### Community resources

- Biostars: [https://www.biostars.org/](https://www.biostars.org/)
- StackOverflow: [https://stackoverflow.com/](https://stackoverflow.com/)
- Twitter Bioinformatics: [https://twitter.com/i/communities/1506791236987879425](https://twitter.com/i/communities/1506791236987879425)

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## Learner assessment

**How would you rate yourself in the following areas?**

*Add a '+' sign to indicate where you think you are*

1. Overall I rate my computational skills:

- **Novice**:++
- **Beginner**: ++++
- **Intermediate**:+++++++
- **Advanced**: +

2. How familiar are you with Linux?

- **I have used it** ++
- **I have tried it but know very little** ++++
- **I'm not an expert but can do everything I need** ++++++*
- **I use it everyday**+

3. How familiar are you with Python?

- **I have used it**+++
- **I have tried it but know very little** ++++++++
- **I'm not an expert but can do everything I need** ++
- **I use it everyday** +

**In a few sentences, what is your biggest computational challenge?**

- **Chosen**: 1. Currently working on a makeflow pipeline for analyzing RNA-Seq for identifying post transcriptional modifications and long non-coding RNA 2. Having difficuty in teaching myself R and Python.

- **Jason**:
- **Henriette**: writing scripts for R by myself; using AlphaFold more efficiently
- **Rachel**: coming up with a question to answer using computational methods
- **Courtney:** I have a background in human genetics bioinformatics, but i am unsure how to know which tools and pipelines to use in plants. I am pretty good at writing scripts myself, but have issues with command line coding/troubleshooting programs.
- Nadia: Work on gen regulatory networks of metal homeostasis
- **Florencia**: finding a robust way of defining pseudogenes.
- **Rucha**: haven't used computational tools but would like to learn about it.
- **Taryn**: currently trying to perform a permutation test to compare the Fst values of sets of genes. Doing in this in R but also want to improve my command line scripting.
- **David**: Finding time to develop models to learn from protein structure. I recently discovered that I like cats and they like me.
- **Will:** I think one of my main challenges is knowing if the scripts I write to answer my research questions are "correct" or "kosher" enough to be accepted by those who are more experienced.
- Jennifer: distributing tools to process big data--best python packaging practices to make tools easy to install and use
- **Bryan**: Allele-specific expression analysis, genomics data visualization. #i love rmarkdown
**Guanghui**:
learning bioinformatics tool; install softwares in the linux system

- **Jacopo**: predict effects of mutations on TFs.

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## Notes

> wget http://swcarpentry.github.io/python-novice-gapminder/files/python-novice-gapminder-data.zip
> unzip python-novice-gapminder-data.zip